Fig. 1: NF-κB phylogenetic analysis and highly selective Rel requirement.
From: Stepwise neofunctionalization of the NF-κB family member Rel during vertebrate evolution
a, An unrooted phylogenetic tree was prepared with the RHR amino acid sequences of NF-κB family members from representative invertebrate and vertebrate species. All sequences were from public databases (Supplementary Tables 1 and 2). No thorny shark ortholog of RelA could be identified. Clusters of the five vertebrate family members are colored. b, Scatter plots comparing nascent transcript RNA-seq datasets from lipid-A-expressed genes (RPKM > 3; n = 2,980 genes) in WT versus Rel−/− C56BL/6 macrophages. The plots show the log2 Rel−/− RPKM/WT RPKM ratios (x axis) and the fold induction values at the indicated time point (y axis), with all values representing averages of two independent biological replicates of the time course (the WT and mutant samples were examined in parallel). Plots are shown for the 1 h and 2 h stimulation time points. Genes exhibiting the strongest Rel dependence (fold change >10) are labeled. Vertical dashed lines denote ten-fold difference. All dependent genes were induced at least 15-fold, except Orai2 (2.9-fold). One additional gene that was not reproducibly dependent on Rel (Mir6903) is labeled with an asterisk.
